recipe bioconductor-eegc

Engineering Evaluation by Gene Categorization (eegc)






This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic cells to primary cells based on high throughput gene expression data screened either by DNA microarray or RNA sequencing. The package takes gene expression profiles as inputs from three types of samples: (i) somatic or stem cells to be (trans)differentiated (input of the engineering process), (ii) induced cells to be evaluated (output of the engineering process) and (iii) target primary cells (reference for the output). The package performs differential gene expression analysis for each pair-wise sample comparison to identify and evaluate the transcriptional differences among the 3 types of samples (input, output, reference). The ideal goal is to have induced and primary reference cell showing overlapping profiles, both very different from the original cells.

package bioconductor-eegc

(downloads) docker_bioconductor-eegc



depends bioconductor-annotationdbi:


depends bioconductor-clusterprofiler:


depends bioconductor-deseq2:


depends bioconductor-dose:


depends bioconductor-edger:


depends bioconductor-limma:






depends bioconductor-s4vectors:


depends r-base:


depends r-ggplot2:

depends r-gplots:

depends r-igraph:

depends r-pheatmap:

depends r-r.utils:

depends r-sna:

depends r-wordcloud:



You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-eegc

and update with::

   mamba update bioconductor-eegc

To create a new environment, run:

mamba create --name myenvname bioconductor-eegc

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull<tag>

(see `bioconductor-eegc/tags`_ for valid values for ``<tag>``)

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